Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic initiation factor 4A.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g8393 g8393.t2 TSS g8393.t2 30144189 30144189
chr_2 g8393 g8393.t2 isoform g8393.t2 30144837 30146029
chr_2 g8393 g8393.t2 exon g8393.t2.exon1 30144837 30145488
chr_2 g8393 g8393.t2 cds g8393.t2.CDS1 30144945 30145488
chr_2 g8393 g8393.t2 exon g8393.t2.exon2 30145547 30145794
chr_2 g8393 g8393.t2 cds g8393.t2.CDS2 30145547 30145647
chr_2 g8393 g8393.t2 exon g8393.t2.exon3 30145859 30145916
chr_2 g8393 g8393.t2 exon g8393.t2.exon4 30145982 30146029
chr_2 g8393 g8393.t2 TTS g8393.t2 30146418 30146418

Sequences

>g8393.t2 Gene=g8393 Length=1006
AGTAAATGAAGATTCAGTTTTAGTTTTCATTTATTTTTATGTATTTATTTTATAGCTCGA
GAATTAGCTATTCAAATTCAAAAAGTTGTTCTTGCATTGGGTGACTTTATGCAGACTGAG
TGTCATGCATGTATTGGTGGAACTAACGTTCGTGAAGATATGCGAACGCTTGAACAAGGC
GTAAATGTAGTAGTTGGAACACCAGGTCGTGTATTTGACATGATTCAAAGAAAAGTACTG
AGAACTAACAATATTAAGCTGTTTGTTCTTGATGAAGCCGATGAGATGCTATCGCGTGGA
TTCAAAGATCAAATTCATGATGTATTTAAGACTCTTCCTAATGATGTACAAGTAATCTTA
CTTTCTGCTACTATGCCAGTTGATGTTTTGGAAGTCAGCAAGTATTTTATGCGTGATCCA
GTGAGAATATTGGTCAAAAAAGAAGAGTTGACATTAGAAGGAATTCGACAATTTTATGTT
AATGTTGAGAAAGAAGAATGGAAATTAGGAACATTGTGTGATTTGTATGACACATTGAGT
ATTGCTCAAGCTGTCATTTTCTGTAATACTCGTCGTAAAGTTGAATTTTTAACTGAAGAA
ATGACAAGACAAAACTTTACTGTTTCTGCTATGCATGGAGAAATGGATCAGTTACTGATT
TGCTTGCTCGTGGTATTGATGTGCAGCAAGTCTCATTGGTTATCAACTATGATTTACCAA
ATAATCGAGAAAATTATATTCACAGGTAGATAAATTTTATTCTATAACTATGCATCTGAT
GCAATTTAATTTTAATCAATTTTAGAATTGGTCGAGGTGGCCGCTTTGGACGTAAAGGTG
TTGCTATAAATTTTGTTACAGAAGAAGATAAGCGCACCTTACTCGATATTGAACAATTCT
GCAAAAATCTTTTTTTATTCATTTTTAAATTTTACTGATACTTCTACTATGATAATGACA
AAAAAGAAACCATTGAAAACTGATTGGCAACTTGATCTGTGTTTTT

>g8393.t2 Gene=g8393 Length=214
MQTECHACIGGTNVREDMRTLEQGVNVVVGTPGRVFDMIQRKVLRTNNIKLFVLDEADEM
LSRGFKDQIHDVFKTLPNDVQVILLSATMPVDVLEVSKYFMRDPVRILVKKEELTLEGIR
QFYVNVEKEEWKLGTLCDLYDTLSIAQAVIFCNTRRKVEFLTEEMTRQNFTVSAMHGEMD
QLLICLLVVLMCSKSHWLSTMIYQIIEKIIFTGR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g8393.t2 Gene3D G3DSA:3.40.50.300 - 1 114 1.1E-35
6 g8393.t2 Gene3D G3DSA:3.40.50.300 - 115 183 1.5E-17
2 g8393.t2 PANTHER PTHR24031:SF625 - 3 195 3.6E-84
3 g8393.t2 PANTHER PTHR24031 RNA HELICASE 3 195 3.6E-84
1 g8393.t2 Pfam PF00270 DEAD/DEAH box helicase 4 93 8.1E-23
5 g8393.t2 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 53 61 -
8 g8393.t2 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 107 20.097
4 g8393.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 181 4.36E-33

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005524 ATP binding MF
GO:0003676 nucleic acid binding MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values